Although the house mouse as a common and widely distributed species is probably best-studied among small mammals, there is a lack of fundamental knowledge regarding species identity, morphology and ecology in Mongolia. Consequently, this study provides results of basic biological research on the Mongolian house mouse. A total of 172 specimens have been studied based on samples collected during the period 1962 to 2016. Using genetic and morphological markers, the taxonomic examination resulted in classification as Mus musculus musculus LINNAEUS, 1758. To characterize the Mongolian house mouse, three fur color traits and 23 metric body and skull traits were analyzed. Two obviously different morphotypes were identified: (1) light individuals with a distinct demarcation line, which occur in most parts of the country, (2) dark individuals with a diffuse demarcation line, which are mainly found in the northern part of the Selenge province. Furthermore, these morphotypes differ in five metric body and skull traits. In general, Mongolian house mice seem to be consistent with reference specimens from Eastern Europe according to metric traits, although exhibiting a shorter tail. In Mongolia Mus musculus lives hemisynanthropically. Habitat preferences are human settlements, but also in natural habitats such as oases, dunes and lakeshores. The population epigenetic analysis by using nonmetric cranial traits exposed three main populations: northcentral, southeast, and west. The latter seems to be more isolated from the other populations, probably due to the Altai Mountains as a natural barrier. The resulting epigenetic distances of the Mongolian house mice are rather low in comparison to other rodents, which indicates that house mice are quite talented in terms of dispersal. The western, southern, and eastern populations show lower values of fluctuating asymmetry (6.5 to 9.0 %), than the northern and central populations (11.5 to 13.1 %). Therefore, the latter seems to be more influenced by environmental or genetic stress factors
